# Tags

A tag is a keyword or label that categorizes your question with other, similar questions. Using the right tags makes it easier for others to find and answer your question.

Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackex…
462 questions
if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design…
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a programming language, widely used in bioinformatics
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for questions related to single-cell RNA-seq.
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one of the common binary formats used to store sequence alignment information. Questions should include this tag if they directly pertain to the format itsel…
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Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
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to refer to the alignment of nucleotide or peptide sequences, producing an arrangement that maximizes similarity between sequences.
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should be used for questions specific to sequence file format .fasta. should **not** be used if you just used fasta file, or if the question is more general about sequence formats.
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a text file type used to store information regarding genetic variants.
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to refer to the gene sequence/coding part of the sequence.
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the process of determining the precise order of nucleotides within a DNA molecule.
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organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.
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Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.
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The process of attaching contextual information to a biomolecular (DNA, RNA, or protein) sequence, such as the location of genes, promoters, or repeats in genomic DNA, or the function of a protein.
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the study of evolutionary relationships among biological entities - often species, individuals or genes.
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for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.
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a set of freely available tools for biological computation written in Python.
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For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
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Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
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Single Nucleotide Polymorphisms. How to find them? How to correlate them with other data? How to represent them? What is their distribution?
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Questions about techniques in which the genetic material of a single cell is analysed individually
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use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific …
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Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.
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The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
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The process of discovering variants in individuals starting from sequencing reads. Can be subdivided into germline variant calling and somatic variant calling. Can also be used for the more specific p…
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Questions specific to nanopore sequencing. For general question about long reads, use tag long-reads instead and for questions about specific sequencer use a specific sequencer tag (i.e. minion, gridi…
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a file format use to store short reads and their quality values
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When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).
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sets of defined rules to organise a specific type of data. Common file format in bioinformatics include FASTA, FASTQ, SAM, BAM, VCF.
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Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or tr…
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use for questions regarding plotting and representation of data, combine with tags specific to type of analyses (genome, protein, rna-seq) and language or library (python, R, ggplot2, igv) if applicab…
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Use it when comparing a measure of the expression between two (or more) samples, where the units are relative to the comparison.
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